autoplot(prcomp(t(mcp_zscore_matrix)), data = person_metadata_df, colour = 'person', main = "MCPCounter")

autoplot(prcomp(t(mcp_zscore_matrix)), data = person_metadata_df, colour = 'cell_type', main = "MCPCounter")

autoplot(prcomp(t(cs_zscore_matrix)), data = person_metadata_df, colour = 'person', main = "Cibersort")

autoplot(prcomp(t(cs_zscore_matrix)), data = person_metadata_df, colour = 'cell_type', main = "Cibersort")

pheatmap(
    mcp_zscore_matrix, 
    main = "MCPCounter", 
    annotation_row = mcp_heatmap_row_df,
    annotation_col = mcp_heatmap_col_df,
    scale = "none")

pheatmap(
    cs_zscore_matrix,
    main = "Cibersort", 
    annotation_col = mcp_heatmap_col_df,
    scale = "none")

kable(mcp_result_df)
cell_type CRC01 CRC02 CRC03 CRC04 CRC05 CRC06 CRC07 CRC08 CRC09 CRC10 CRC11
T cells 13.8292755 0.9653426 18.0546530 0.0079474 21.1208562 2.1961531 34.3130702 31.0723570 64.3336642 110.8644786 221.5502480
CD8 T cells 0.1044257 0.0000000 0.1144199 0.0000000 5.1480786 3.5415684 9.9586084 0.0000000 25.4858351 0.0000000 0.0000000
Cytotoxic lymphocytes 2.8650014 0.2164809 0.4099724 0.0000000 5.0368322 0.0000000 127.9298351 0.1132905 3.8932443 53.7292123 5.8935111
NK cells 0.6357623 1.1450994 2.0403135 0.0000000 0.5577085 0.0406549 17.3850143 0.2555213 0.0222527 0.9405487 0.0782516
B lineage 2481.5315250 0.3873194 128.5530097 0.0886628 30.5502987 15.7810464 2.9325842 94.1196600 18.1666949 0.4736888 0.3039038
Monocytic lineage 8.4573807 4.4268619 32.7316174 0.0265289 23.9040232 0.5908418 15.1087143 10.7185267 1.8697219 4.1096415 20.9601860
Myeloid dendritic cells 0.5765238 2.4619812 0.0323942 0.2421462 106.4240804 0.0000000 0.0323203 0.8329225 1.6702145 24.7167584 0.0000000
Neutrophils 20.5790657 22.3305318 18.7862939 8.6250564 6.6263891 13.0897145 27.8710753 12.9548885 24.5172605 2.8520772 182.4263920
Endothelial cells 2.9168239 15.3186873 0.9363362 1.5290548 1.7832275 7.0728664 4.3108516 1.8967228 5.7432010 5.1042425 4.4457599
Fibroblasts 1.5148395 103.9436579 0.3104304 70.6748973 26.8494087 0.0459198 303.8642751 1.0218086 0.4600203 95.1860144 435.0542083 
kable(cs_result_df)
cell_type CRC01 CRC02 CRC03 CRC04 CRC05 CRC06 CRC07 CRC08 CRC09 CRC10 CRC11
B.cells.naive 0.0324249 0.0109948 0.0000000 0.0000000 0.0752762 0.0000000 0.0155335 0.0000000 0.0205709 0.0000000 0.0199688
B.cells.memory 0.0000000 0.0000000 0.0063887 0.0000000 0.0000000 0.0598007 0.0000000 0.0370316 0.0000000 0.0000000 0.0000000
Plasma.cells 0.0473771 0.0000000 0.0008949 0.0000000 0.0293307 0.0044725 0.0090820 0.0155085 0.0000000 0.0101017 0.0062959
T.cells.CD8 0.5361031 0.0006400 0.0183396 0.0000000 0.1673104 0.0000000 0.1920935 0.0106082 0.1732509 0.0414166 0.0000000
T.cells.CD4.naive 0.0000000 0.1286951 0.0000000 0.0370675 0.0000000 0.2217144 0.0000000 0.0116718 0.0000000 0.0000000 0.0000000
T.cells.CD4.memory.resting 0.0000000 0.0445111 0.0179172 0.3154697 0.1766933 0.2540471 0.0000000 0.4148627 0.4841043 0.1484929 0.2049672
T.cells.CD4.memory.activated 0.0893417 0.0000000 0.0000000 0.0000000 0.0795550 0.0000000 0.0658341 0.3356031 0.1180163 0.0148216 0.2507235
T.cells.follicular.helper 0.0470317 0.0000000 0.0175408 0.0000000 0.0000000 0.0000000 0.0299156 0.0000000 0.0568229 0.0355081 0.0665547
T.cells.regulatory..Tregs. 0.0000000 0.0000000 0.0000000 0.0813446 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
T.cells.gamma.delta 0.0022534 0.0000000 0.0610650 0.0793380 0.0000000 0.2062707 0.0239566 0.0000000 0.0279861 0.0000000 0.0056172
NK.cells.resting 0.0000000 0.0719079 0.0000000 0.0000000 0.0187349 0.0000000 0.0000000 0.0323334 0.0642258 0.0000000 0.0000000
NK.cells.activated 0.0373345 0.0000000 0.0481145 0.0398817 0.0000000 0.0000000 0.3295948 0.0000000 0.0000000 0.4159811 0.1229230
Monocytes 0.0128247 0.4244302 0.0000000 0.0000000 0.0103271 0.0000000 0.0034563 0.0163080 0.0043653 0.0136778 0.0100214
Macrophages.M0 0.0000000 0.1487772 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Macrophages.M1 0.0000000 0.0000000 0.0000000 0.0448319 0.0000000 0.0059163 0.0000000 0.0000000 0.0000000 0.0000000 0.0069890
Macrophages.M2 0.0226498 0.0388808 0.0893910 0.0000000 0.0924293 0.0039942 0.0151936 0.0083860 0.0001223 0.0090362 0.0245820
Dendritic.cells.resting 0.0040118 0.0000000 0.0000000 0.0000000 0.1143003 0.0000000 0.0000000 0.0061772 0.0000000 0.0090394 0.0107591
Dendritic.cells.activated 0.0000000 0.0000000 0.0350956 0.0583733 0.0729468 0.0358320 0.0060190 0.0007664 0.0072328 0.0313241 0.0071882
Mast.cells.resting 0.0000000 0.0000000 0.0000000 0.0000000 0.0591832 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
Mast.cells.activated 0.1520148 0.0542089 0.6713359 0.2283382 0.0068086 0.1826323 0.2897604 0.1107432 0.0256478 0.2517119 0.2442204
Eosinophils 0.0166326 0.0769540 0.0250936 0.1153551 0.0961636 0.0253198 0.0122401 0.0000000 0.0176545 0.0176363 0.0168808
Neutrophils 0.0000000 0.0000000 0.0088232 0.0000000 0.0009409 0.0000000 0.0073205 0.0000000 0.0000000 0.0012523 0.0023088
P.value 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000 9999.0000000
Correlation 0.1222714 0.0290433 0.1093780 0.0117757 0.2109025 -0.0004476 0.5804317 0.1731422 0.2737427 0.3564176 0.4973030
RMSE 1.0865307 1.0929230 1.2344680 1.1165663 0.9915465 1.1306945 0.8319734 1.0365532 1.0157390 1.0237864 0.8683398